Structure of PDB 5ndj Chain 65 Binding Site BS01

Receptor Information
>5ndj Chain 65 (length=111) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ARLTAYERRKFRVRNRIKRTGRLRLSVFRSLKHIYAQIIDDEKGVTLVSA
SSLALKLKGNKTEVARQVGRALAEKALALGIKQVAFDRGPYKYHGRVKAL
AEGAREGGLEF
Ligand information
>5ndj Chain 14 (length=2909) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
ggucaagaugguaagggcccacgguggaugccucggcacccgagccgaug
aaggacguggcuaccugcgauaagccagggggagccgguagcgggcgugg
aucccuggauguccgaaugggggaacccggccggcgggaacgccggucac
cgcgcuugcgcggggggaaccuggggaacugaaacaucucaguacccaga
ggagaggaaagagaaaucgacucccugaguagcggcgagcgaaaggggac
cagccuaaaccguccggcuuguccgggcggggucguggggcccucggaca
ccgaauccccagccuagccgaagcuguugggaagcagcgccagagagggu
gaaagccccguaggcgaaagguggggggauaggugaggguacccgaguac
cccgugguucguggagccaugggggaaucugggcggaccaccgccuaagg
cuaaguacuccgggugaccgauagcgcaccaguaccgugagggaaaggug
aaaagaaccccgggaggggagugaaauagagccugaaaccgugggcuuac
aagcagucacggccccgcaagggguuguggcgugccuauugaagcaugag
ccggcgacucacggucgugggcgagcuuaagccguugaggcggaggcgua
gggaaaccgaguccgaacagggcgcaaacggcccgcacgcgggccgaaaa
guccgcggccguggacccgaaaccgggcgagcuagcccuggccaggguga
agcuggggugagacccaguggaggcccgaaccggugggggaugcaaaccc
cucggaugagcuggggcuaggagugaaaagcuaaccgagcccggagauag
cugguucuccccgaaaugacuuuagggucagccucaggcgcugacugggg
ccuguagagcacugauagggcuagggggcccaccagccuaccaaacccug
ucaaacuccgaagggucccagguggagccugggagugagggcgcgagcga
uaacguccgcguccgagcgcgggaacaaccgagaccgccagcuaaggccc
ccaagucugggcuaagugguaaaggauguggcgccgcgaagacagccagg
auguuggcuuagaagcagccaucauuuaaagagugcguaauagcucacug
gucgaguggcgccgcgccgaaaaugaucggggcuuaagcccagcgccgaa
gcugcgggucugggggaugaccccaggcgguaggggagcguucccgaugc
cgaugaaggccgacccgcgagggcggcuggagguaagggaagugcgaaug
ccggcaugaguaacgauaaagagggugagaaucccucucgccguaagccc
aaggguuccuacgcaauggucgucagcguaggguuaggcgggaccuaagg
ugaagccgaaaggcguagccgaagggcagccgguuaauauuccggcccuu
cccgcaggugcgauggggggacgcucuaggcuagggggaccggagccaug
gacgagcccggccagaagcgcagggugggagguaggcaaauccgccuccc
aacaagcucugcgugguggggaagcccguacgggugacaaccccccgaag
ccagggagccaagaaaagccucuaagcacaaccugcgggaacccguaccg
caaaccgacacaggugggcgggugcaagagcacucaggcgcgcgggagaa
cccucgccaaggaacucugcaaguuggccccguaacuucgggagaagggg
ugcucccuggggugaugagccccggggagccgcagugaacaggcucuggc
gacuguuuaccaaaaacacagcucucugcgaacucguaagaggagguaua
gggagcgacgcuugcccggugccggaaggucaaggggaggggugcaagcc
ccgaaccgaagccccggugaacggcggccguaacuauaacgguccuaagg
uagcgaaauuccuugucggguaaguuccgaccugcacgaaaagcguaacg
accggagcgcugucucggcgagggacccggugaaauugaacuggccguga
agaugcggccuacccguggcaggacgaaaagaccccguggagcuuuacug
cagccugguguuggcucuuggucgcgccugcguaggauaggugggagccu
gugaacccccgccuccgggugggggggaggcgccggugaaauaccacccu
ggcgcggcugggggccuaacccucggauggggggacagcgcuuggcgggc
aguuugacuggggcggucgccuccuaaaagguaacggaggcgcccaaagg
uccccucaggcgggacggaaauccgccggagagcgcaaggguagaagggg
gccugacugcgaggccugcaagccgagcaggggcgaaagccgggccuagu
gaaccgguggucccguguggaagggccaucgaucaacggauaaaaguuac
cccggggauaacaggcugaucucccccgagcguccacagcggcggggagg
uuuggcaccucgaugucggcucgucgcauccuggggcugaagaagguccc
aaggguugggcuguucgcccauuaaagcggcacgcgagcuggguucagaa
cgucgugagacaguucggucucuauccgccacgggcgcaggaggcuugag
gggggcucuuccuaguacgagaggaccggaagggacgcaccucugguuuc
ccagcugucccuccaggggcauaagcuggguagccaugugcggaagggau
aaccgcugaaagcaucuaagcgggaagcccgccccaagaugaggccuccc
acggcgucaagccgguaaggacccgggaagaccacccgguggaugggccg
gggguguaagcgccgcgaggcguugagccgaccggucccaaucguccgag
gucuugacc
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<<<<<..>>>>>>.>>....<<<<<.....<......>......>>>>>.
..........<<....>>...<<<<<.....<<.....>>....>>>>>.
..<<<....<<<<<<<<.....>>>>>>>>......<<<<<<<<.....<
<<...<<<<<.<<<<.<<<...<<<<<......>>>>>((......<<<.
....))>>>...>>>...>>>>..>>>>>..>>>.>>>>>.>>>.....<
<<<<<<<<.......>>>>>>>>>......<<<<<..((((>>>>>..>>
>......>>.>>>>>>.>>...............<<....>>....>>..
.......<<<<....>>>>..................>>>>>>>>>>>..
.....<<<<<<<<<<<....>>>>>>>>>>>...<............>.<
<<<<<....<<<<<<<<<<<<<..<<<...<<<.....>>>...>>>...
<<....>>..<<<<.....>>>>.....<<<<..........>>>>....
>>>>>>>>>>>>>..<<.<...<<<<<<.....<<<<<<<<<..<<<...
.<<<<<<......>>>>>>.....>>>...<<<<.<<<<........>>>
>>>>>....>>>>>>>>>...<<<.....>>>......>>>>>>......
>.>>..<<<<<<....<<<<<....>>>>><<<<<<<<<.....<<<<<<
<<<...<<<...<<<<<<<<...<<.<<........>>..>>...>>>>>
>>>..>>.>...>>>>>>>>>.....>>>>>>>.>>..<<<<<<<.<<..
....>>.>>>>>>>.....<<<......>>>...<<<<.<<<...<<<((
(.....<<<<<<...........<<..<<<<<<<<<......<.<<<<<.
<<.....................>>.........<........>...>>>
>>.>..>>>>>>>>>.>>..........)))......>>>>>>.>>>...
>>>>>>><<<<<<<<.....>>>>>>>>....>>>>>>..<<<<<...<<
<......<<<<<.<<<....>>>>>>>>...>>>..>>>>>........>
>>>>><......<<.....<<<<<<.......>>>>>><<<<....<<<<
<.<<...<<<<<<...<<.....>>.>>>>>>....((<<<<.<<...<<
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<<<<<<<<<<<...<<<<....<<<<<.<<<..<<<<<.<<<<.<<..[[
[[...>>>>>><<<...<<<<<<<<<<<<<<<<.<<.....>>>>>>>>>
.....>>>>>>>>>..>>><...<<<<....>>>>.....>>>>>>...>
>>..>>>>>.........>>>>...>>...>>>>>>>>>>>>>>>..>>.
....<<......>>>>>>>.<<<<<....>>>>>..>>>>..<<<<....
<<<<<<<<.<<.........<.....<<<<<.....<..>......>>>>
><<<<<<<<<<<<.....>>>>>>>>>>>>............<<<<<<<<
<..<<<.........>>>..<<<<<<<.....<<<....>>>.......>
>>>>>>.<<<<<.<<<..<<<<<<<..<<<...<<...<<<<<....>>>
>>...>>...>>>>>>>>..>>>>><<<<<<.......>>>>>>......
..<...........<<<<<<.....>>>>>>.....>....>>>>>..>>
.>>>>>>>..>..>>.>>>>>>>>.>>>>>>.....>.....<<<<<...
.....>>>>>..<<<<<<<<.<<<.........<<<<.<<<<<<..<<<<
<.<<<.<<<<<.<<<<<<<<<<<<<<<<...........<<.......<.
.......<<<<<<<..>>>>>>>.....>.................>>..
>>>>>>>>>>>>>>>>...<<<<<....>>>>>....>>>>>.>>>..>>
>>>..<<<<.....>>>><<<<<<...........>>>>>>..<<...<<
<<<<<...<<<<<<.......>>>>>>.....<<...(((>>....>>>>
>>>...<<<<..<<<......>>>..>>>>.<<<....>>>.>>)))...
....<<<<<<<.<<..))))..>>>>>>>>>.............>>>>..
>>>>>>.......<<<<...<<<<<<...<<.......>>...>>>>>>.
...>>>.>.......<<<<<.<<<<<<..<<<<<<<<<......>>>>>>
..>>>.<<<<<.....>>>>>.....>>>>>..>...>>>.>>....<<<
<<<<....>>>.>>>>........>>>>>>>>>>>....<<<<<<<...<
<<<..<<<<<<<...............>>>>>>>.<<<<<...<<<<...
<<<<<<<<<<<]]]]>>>>>>...>>>>>...>>>>.>>>>>...<<<..
..<<<<<...........>>>>>....>>>.>>>>.......>>>>>>>.
...<.......>......<<<<<<<<<.......>>>>>....<<<<<<<
<.<<<....<<<<<....>>>>>...>>>..>>>>>.>>>...>>>>...
.>>>>>>>.
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5ndj Aminoglycoside interactions and impacts on the eukaryotic ribosome.
Resolution3.15 Å
Binding residue
(original residue number in PDB)		A2 R3 R9 R10 F12 R13 N16 R17 T21 R23 F87 R89 Y94 E111 F112
Binding residue
(residue number reindexed from 1)		A1 R2 R8 R9 F11 R12 N15 R16 T20 R22 F86 R88 Y93 E110 F111
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
GO:0008097 5S rRNA binding
GO:0019843 rRNA binding
Biological Process
GO:0006412 translation
Cellular Component
GO:0005737 cytoplasm
GO:0005840 ribosome
GO:0022625 cytosolic large ribosomal subunit
GO:1990904 ribonucleoprotein complex

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5ndj, PDBe:5ndj, PDBj:5ndj
PDBsum5ndj
PubMed29208708
UniProtQ5SHQ4|RL18_THET8 Large ribosomal subunit protein uL18 (Gene Name=rplR)

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